Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.67 kDa 
• Atom Count: 5721 
• Residue Count: 727 
• Unique protein chains: 3

4KFM

Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with the beta-gamma G protein subunits

• DOI: 10.2210/pdb4KFM/pdb

• Classification: METAL TRANSPORT
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Komagataella pastoris, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-04-27 Released: 2013-06-12 
• Deposition Author(s): Whorton, M.R., MacKinnon, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.265 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Literature

X-ray structure of the mammalian GIRK2-beta gamma G-protein complex.

Whorton, M.R., MacKinnon, R.

(2013) Nature 498: 190-197

• PubMed: 23739333 
• DOI: 10.1038/nature12241
• Primary Citation of Related Structures:  
  4KFM


• PubMed Abstract: 
  

G-protein-gated inward rectifier K(+) (GIRK) channels allow neurotransmitters, through G-protein-coupled receptor stimulation, to control cellular electrical excitability. In cardiac and neuronal cells this control regulates heart rate and neural circuit activity, respectively. Here we present the 3.5 Å resolution crystal structure of the mammalian GIRK2 channel in complex with βγ G-protein subunits, the central signalling complex that links G-protein-coupled receptor stimulation to K(+) channel activity. Short-range atomic and long-range electrostatic interactions stabilize four βγ G-protein subunits at the interfaces between four K(+) channel subunits, inducing a pre-open state of the channel. The pre-open state exhibits a conformation that is intermediate between the closed conformation and the open conformation of the constitutively active mutant. The resultant structural picture is compatible with 'membrane delimited' activation of GIRK channels by G proteins and the characteristic burst kinetics of channel gating. The structures also permit a conceptual understanding of how the signalling lipid phosphatidylinositol-4,5-bisphosphate (PIP2) and intracellular Na(+) ions participate in multi-ligand regulation of GIRK channels.

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Organizational Affiliation: 

Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G protein-activated inward rectifier potassium channel 2	A	340	Mus musculus	Mutation(s): 0  Gene Names: Kcnj6, Girk2, Kcnj7, W
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Channels: Potassium, Sodium, & Proton Ion-Selective	Protein:  GIRK2 (Kir3.2) G-protein-gated K+ channel in complex with βγ G-protein subunits
Find proteins for P48542 (Mus musculus) Explore P48542  Go to UniProtKB:  P48542
NIH Common Fund Data Resources
IMPC  MGI:104781

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	340	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
NIH Common Fund Data Resources
PHAROS  P62873 GTEx  ENSG00000078369

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	70	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Channels: Potassium, Sodium, & Proton Ion-Selective	Protein:  GIRK2 (Kir3.2) G-protein-gated K+ channel in complex with βγ G-protein subunits
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
NIH Common Fund Data Resources
PHAROS  P59768 GTEx  ENSG00000186469

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PIO	A	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C25 H49 O19 P3 XLNCEHRXXWQMPK-MJUMVPIBSA-N
LMT	A	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.265 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.308	α = 90
b = 127.308	β = 90
c = 309.392	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-27 
• Released Date: 2013-06-12 
Deposition Author(s): Whorton, M.R., MacKinnon, R.

Revision History 

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2013-09-11
  Changes: Database references